A federal judge levied a heavy $5.9 million fine yesterday against a Manhattan VA hospital after docs there botched a weight-loss operation on a 500-pound man who died from complications.

Brooklyn federal Judge Leo Glasser said the hospital’s “egregious” malpractice caused Warren Jupiter’s pain and suffering, and led to his death in 2005 at age 54.

Glasser awarded Jupiter’s widow, Barbara, $5 million and their three children a total of $900,000 after he said doctors failed to find a gastric leak because they thought he was too large to receive a CAT scan that would have likely diagnosed the problem, according to court papers.

“The guy was too heavy for the carriage of the CAT scan,” according to testimony.

At one point, doctors said they considered sending Jupiter to the Bronx Zoo, where an exam table was equipped for a “large-capacity” patient.